R Observatory: Metrics for SPECK version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SPECK

1.0.1

Receptor Abundance Estimation using Reduced Rank Reconstruction and Clustered Thresholding

1packages depend

2.9Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Azka JavaidFirst published 2022-10-134 releasesCRAN page ↗

Surface Protein abundance Estimation using CKmeans-based clustered thresholding ('SPECK') is an unsupervised learning-based method that performs receptor abundance estimation for single cell RNA-sequencing data based on reduced rank reconstruction (RRR) and a clustered thresholding mechanism. Seurat's normalization method is described in: Hao et al., (2021) doi:10.1016/j.cell.2021.04.048, Stuart et al., (2019) doi:10.1016/j.cell.2019.05.031, Butler et al., (2018) doi:10.1038/nbt.4096 and Satija et al., (2015) doi:10.1038/nbt.3192. Method for the RRR is further detailed in: Erichson et al., (2019) doi:10.18637/jss.v089.i11 and Halko et al., (2009) doi:10.48550/arXiv.0909.4061. Clustering method is outlined in: Song et al., (2020) doi:10.1093/bioinformatics/btaa613 and Wang et al., (2011) doi:10.32614/RJ-2011-015.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("SPECK", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-speck

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-SPECK

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-SPECK

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 8.0 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

75%

Documentation · exports

5

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-03-30
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.9K

CRAN downloads in the past year

Rank #12,493 · ~8/day · ~238/mo

Releases R versions

Daily download trend is not available in this view yet.

15330 days

81690 days

2.9K1 year

Compare downloads with other packages →

Also on207 r2u2 autocran

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (5)

Ckmeans.1d.dp magrittrMatrixrsvd Seurat

LinkingTo (0)

none

Suggests (6)

ggplot2 gridExtra knitr rmarkdown SeuratObject usethis

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

STREAK

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Azka Javaid

Author, Maintainer

Authors (2)

Azka Javaid

Author, Maintainer

H. Robert Frost

Author

Package Timeline

4 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.1Latest
2025-10-05 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.0
2023-11-17 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.1.1
2022-10-16 · diff ↗
0.1.0
2022-10-13
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-10-13
Total releases: 4 / 4 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5
Bundled data: 1.9 MB / 1 file
Download size: 2.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SPECK")

Format

Javaid, A., & Frost, H. R. (2025). SPECK: Receptor Abundance Estimation using Reduced Rank Reconstruction and Clustered Thresholding (Version 1.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.SPECK

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for SPECK version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-08-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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